In the object editor under abilities go to the spell you are making and look for the field that says "Required Level" it is normally set to 1,
and ultimates are set to level 6. Set it to whatever you want. There is also a field called "level skip requirement", which is normally set to zero.
If you change it to anything greater than 0, lets say 3, then you can only level the ability once every 3 levels.
Example:
Your custom spell -
Level requirement: 2
Level skip requirement: 3
Levels: 2
When you look at this skill ingame and you open your hero ability menu and hover over the ability, it will say "spell level 1 - requires hero level 2"
when you hit level 2 and open the ability menu again and learn the level 1 ability, it will now tell you "spell level 2 - requires hero level 5"
Hope this clears everything up.